[9] He completed his postgraduate study at the University of London,[8] where he was awarded a PhD in pharmacology, for research investigating the characterisation of prostaglandin E2 release induced by interleukin-1 in human synovial cells, in 1988.

[9] O'Neill's research investigates inflammation, a highly complex process that is provoked in the body during infection by bacteria and viruses but also in response to major trauma and injury.

Inflammation restores us to health but for largely unknown reasons it can go rogue and give rise to a whole range of inflammatory diseases which remain difficult to treat.

He has uncovered new molecules and biochemical processes that are triggered by sensors of infection and tissue injury, including the toll-like receptors[12][13][14][15] and inflammasomes, and the signals they drive that stimulate inflammation, notably cytokines in the interleukin-1 family.

[2] He has co-founded Inflazome with Matt Cooper which developed NLRP3 inhibitors and was acquired by Roche Ltd in 2020, and Sitryx with Houman Ashrafian, Johnathan Powell, Jeff Rathmell and Mike Rosenblum.

He was elected a member of the Royal Irish Academy (MRIA) in 2004[17] and the European Molecular Biology Organisation (EMBO) in 2005.

In 2021 he published Keep Calm and Trust the Science: A Remarkable Year in the Life of an Immunologist, which is his diary covering the COVID-19 pandemic.